Perhaps the real issue is how we interpret the meaning of the term "timeout". What is a timeout? And how many timeouts are we allowed during a match.
If a timeout is defined as the act of allowing the clock to run out of time, then yes, after allowing it to expire a second time you would be done, game over. If, however interpret the timeout as the ability to run the shot timer to zero AND have the clock reset, then yes, after allowing it to expire the second time you should get the clock reset again and be allowed to continue the match.
Which now leads to the arguement of how many timeouts do we have during a match, one or two. Well, if you believe a timeout is the expiration of time allowed to complete a shot, then we would have two timeouts total, with one remaining after allowing the clock to expire the first time. If you run the clock down to zero a second time, then that's it, game over.
On the other hand you feel the timeout is defined as the grace period granted after you've allowed the shot clock to expire and then can continue to play with a new timer to attempt the shot, then indeed there are no timeouts remaining after ther first one. You would not have one timeout remaining, and if you run the clock down again, you won't get that grace period to think things over before continuing on with yet another shot clock. You're done, end of game.
So really, it comes down to what is a timeout as defined by the authority (WGT and their software development group). I think we know what they think. I've got better things to do than try to get the world to conform to one interpretation of a word since we all know words can take on multiple meanings in their usage regardless of language used to express them. Let's just agree to disagree and move on to better things.
Remember, in life when your time is up, there's no life remaining (other than the afterlife if you believe it exists) and its "game over" folks. Unfortunately, we don't get to see the timer!